You’re getting burned by the confusion that occurs when you add a clip that’s a different size to the project frame. kdenlive will try to automatically make it still fill the frame. Then when you start doing things like adding a transform it turns into a confused mess as to which coordinate system it’s actually working on and what the “size” percentage is actually relative to (doubly so if the aspect ratios differ and X was rescaled differently to Y). If you add another transform, that all just compounds.
There’s probably a whole bunch of ways that ought to be improved, but you are starting on pretty fragile ground if you’re mixing different source formats.
Right now, my best advice is if your project is 1080p, and you want effects to behave predictably, make your source image 1920x1080, pre-scaled how you want to fit it into that frame, before you add it to the project. Then you can layer transforms and other effects as deep as you like and it should all work as you expect.